The derby and third place went to the hosts thanks to a goal in injury time as the Yellow Submarine will now be forced to fight for La Liga survival on the final day
After drawing 2-2 earlier in the season in a competitive, physical match, it was a similar story in this encounter, with both teams producing quality chances but the goalkeepers were the heroes before the Brazilian attacker struck late to secure victory. The three points ensured Los Che enter the final matchday next weekend six points clear of Malaga as Unai Emery's men confirmed third place in the league and automatic Champions League qualification.
Both teams had chances in the opening minutes, although most were long-range, ambitious attempts that were dealt with comfortably by the shot-stoppers, as Vicente Guaita and Diego Lopez were in fine form from the start.
However, the middle and latter stages of the opening period quickly went by with few chances. Each team had potentially dangerous set-piece opportunities, but the defences were alert and attentive as the break arrived with the teams standing just as they had started.
Early on in the second half, Aritz Aduriz appeared certain to put the hosts in front with a close-range volley, but Lopez was again there to keep the game scoreless with a reflex save, while Pablo Piatti missed another attempt from point-blank moments later.
On 58 minutes, it was the visitors who came close to breaking the deadlock as Borja Valero used a clever cut at the top of the box to evade a defender before blasting a left-footed drive just wide of the right post that left Guaita frozen.
As the game neared its end, it was all Valencia in attack. On 67 minutes, Emery's side went on the counter as Piatti played a soft, low ball to the right side of the box for an on-coming Pablo Hernandez, but the winger's sliding effort was derailed at the front post by Lopez, who got just enough on the shot to send it out for a corner.
Both teams tightened up in defence as the clock ticked down, eliminating various threats with long clearances. Aduriz did have a look-in when he slipped through for a header off a ball by Ricardo Costa seven minutes from time, but again Lopez was there to deny Valencia. The Villarreal shot-stopper was then saved by the post minutes later after Pablo Hernandez was presented with a clear-cut opening.
The breakthrough finally came in the 91st minute. After a long free kick was sent into the box by Jordi Alba and headed down by Aduriz, Jonas trapped with his chest and turned his marker before finishing with aplomb into the left side of the goal.
With the result, Los Che seal third place with 61 points, while the Yellow Submarine are in 16th spot with 41 points, just one point above the relegation zone.
Valencia will close out the season at Real Sociedad next weekend, while Villarreal will play host to Atletico Madrid.